[Insight-users] how to get the buffer data
Ali Habib
ali.mahmoud.habib at gmail.com
Wed Dec 29 05:17:49 EST 2010
Sorry for disturbance,
but I have
ImageType::Pointer image_1 = reader->GetOutput() ;
I misunderstand how to get the pixel type of image_1 , using the 2 options
you gave me . could u give me more details
Best regards
On Tue, Dec 28, 2010 at 11:26 AM, Dan Mueller <dan.muel at gmail.com> wrote:
> Hi Ali,
>
> Try the following to get the image buffer as a pointer:
> InputPixelType* buffer = image_1->GetBufferPointer();
>
> You can then treat the buffer as a simple pointer (e.g. cast to
> unsigned char *, whatever).
>
> Determining if the pixel type is scalar or not is a little trickier.
> At first glance the method
> itk::ImageBase::GetNumberOfComponentsPerPixel() seems helpful, but it
> does not work as you might expect (see documentation). I'm not sure if
> there is a better way, but I use a specialized traits class to help
> (see below). You use the class as follows:
> InputPixelType pixel;
> unsigned int numComponents =
> itk::VectorPixelTraits<InputPixelType>::GetNumberOfComponents(pixel);
>
> HTH
>
> Cheers, Dan
>
> /*=========================================================================
>
> Program: Insight Segmentation & Registration Toolkit
> Module: $RCSfile: itkVectorPixelTraits.h,v $
> Language: C++
> Date: $Date$
> Version: $Revision$
>
> Copyright (c) Insight Software Consortium. All rights reserved.
> See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for
> details.
>
> This software is distributed WITHOUT ANY WARRANTY; without even
> the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE. See the above copyright notices for more information.
>
> =========================================================================*/
> #ifndef __itkVectorPixelTraits_h
> #define __itkVectorPixelTraits_h
>
> #include "itkMacro.h"
> #include "itkArray.h"
> #include "itkVector.h"
> #include "itkFixedArray.h"
> #include "itkRGBPixel.h"
> #include "itkRGBAPixel.h"
> #include "itkVariableLengthVector.h"
> #include "itkNumericTraits.h"
>
> namespace itk
> {
>
> /** \class VectorPixelTraits
> * \brief Define additional traits for vector pixels (eg. fixed array,
> RGB).
> *
> * VectorPixelTraits is used to extend the traits associated with vector
> pixel
> * types such as fixed array, RGBPixel, VariableLengthVector, and so on.
> * These traits also support scalar types (such as unsigned char, short)
> * so that both vector and scalar types can be treated in a unified way.
> *
> * Note this default implementation defines traits for all scalar types
> * (eg. unsigned char, short, double, etc).
> *
> * \ingroup DataRepresentation
> */
> template <class T>
> class VectorPixelTraits {
> public:
> /** Get the number of components for the given type.
> * An input is required for variable length types whose
> * length is defined at run-time rather than compile-time.
> * For other types the input is simply ignored. */
> static unsigned int GetNumberOfComponents( T input ) { return 1; }
>
> /* Return the reference to the given indexed element in the vector. */
> static T *GetElement( unsigned int i, T *pixel ) { return pixel; }
>
> /* Set the value of the left element with the value of the right. */
> static void SetElement( unsigned int i, T &left, T right ) { left = right;
> }
>
> /* Return the zero value. */
> static T ZeroValue( T input ) { return NumericTraits<T>::ZeroValue(); }
>
> /* Convert the given double to the pixel type.
> NOTE: This is not implemented for VariableLengthVectors! */
> static T Convert( double input ) { return static_cast<T>(input); }
> };
>
> /** Define a macro to be used for RGB types. */
> #define RGBSTATICTRAITSMACRO( T, E ) \
> template<> \
> class VectorPixelTraits< T<E> > { \
> public: \
> static unsigned int GetNumberOfComponents( T<E> input ) \
> { return 3; } \
> static E *GetElement( unsigned int i, T<E> *pixel ) \
> { return &((*pixel)[i]); } \
> static void SetElement( unsigned int i, T<E> &left, T<E> right ) \
> { left[i] = right[i]; } \
> static T<E> ZeroValue( T<E> input ) \
> { return NumericTraits<T<E>>::ZeroValue(); } \
> static T<E> Convert( double input ) \
> { T<E> value( static_cast<E>(input) ); return value; } \
> }; \
>
> RGBSTATICTRAITSMACRO( RGBPixel, unsigned char );
> RGBSTATICTRAITSMACRO( RGBPixel, signed char );
> RGBSTATICTRAITSMACRO( RGBPixel, unsigned short );
> RGBSTATICTRAITSMACRO( RGBPixel, signed short );
> RGBSTATICTRAITSMACRO( RGBPixel, unsigned long );
> RGBSTATICTRAITSMACRO( RGBPixel, signed long );
> RGBSTATICTRAITSMACRO( RGBPixel, float );
> RGBSTATICTRAITSMACRO( RGBPixel, double );
>
> /** Define a macro to be used for RGBA types. */
> #define RGBASTATICTRAITSMACRO( T, E ) \
> template<> \
> class VectorPixelTraits< T<E> > { \
> public: \
> static unsigned int GetNumberOfComponents( T<E> input ) { return 4; } \
> static E *GetElement( unsigned int i, T<E> *pixel ) { return
> &((*pixel)[i]); } \
> static void SetElement( unsigned int i, T<E> &left, T<E> right ) {
> left[i] = right[i]; } \
> static T<E> ZeroValue( T<E> input ) { T<E> zero =
> NumericTraits<T<E>>::ZeroValue(); zero.SetAlpha( 254 ); return zero; }
> \
> static T<E> Convert( double input ) { T<E> value(
> static_cast<E>(input) ); return value; } \
> }; \
>
> RGBASTATICTRAITSMACRO( RGBAPixel, unsigned char );
> RGBASTATICTRAITSMACRO( RGBAPixel, signed char );
> RGBASTATICTRAITSMACRO( RGBAPixel, unsigned short );
> RGBASTATICTRAITSMACRO( RGBAPixel, signed short );
> RGBASTATICTRAITSMACRO( RGBAPixel, unsigned long );
> RGBASTATICTRAITSMACRO( RGBAPixel, signed long );
> RGBASTATICTRAITSMACRO( RGBAPixel, float );
> RGBASTATICTRAITSMACRO( RGBAPixel, double );
>
> /** Define a macro to be used for all (fixed) array types. */
> #define FIXEDARRAYSTATICTRAITSMACRO( T, E, N ) \
> template<> \
> class VectorPixelTraits< T<E,N> > { \
> public: \
> static unsigned int GetNumberOfComponents(T<E,N> input) { return N; } \
> static E *GetElement( unsigned int i, T<E,N> *pixel) { return
> &((*pixel)[i]); } \
> static void SetElement( unsigned int i, T<E,N> &left, T<E,N> right)
> { left[i] = right[i]; } \
> static T<E,N> ZeroValue( T<E,N> input ) { T<E,N> zero; zero.Fill(
> NumericTraits<E>::ZeroValue() ); return zero; } \
> static T<E,N> Convert( double input ) { T<E,N> value; value.Fill(
> static_cast<E>(input) ); return value; } \
> }; \
>
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 1 );
>
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 2 );
>
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 3 );
>
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 4 );
>
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 1 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 1 );
>
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 2 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 2 );
>
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 3 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 3 );
>
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 4 );
> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 4 );
>
> /** Define a macro to be used for all (variable) array types. */
> #define VARIABLEARRAYSTATICTRAITSMACRO( T, E ) \
> template<> \
> class VectorPixelTraits< T<E> > { \
> public: \
> static unsigned int GetNumberOfComponents(T<E> input) { return
> input.Size(); } \
> static E *GetElement( unsigned int i, T<E> *pixel) { return
> &((*pixel)[i]); } \
> static void SetElement( unsigned int i, T<E> &left, T<E> right) {
> left[i] = right[i]; } \
> static T<E> ZeroValue( T<E> input ) { return
> NumericTraits<T<E>>::Zero(input); } \
> static T<E> Convert( double input ) { T<E> value; /* NOT IMPLEMENTED
> */ return value; } \
> }; \
>
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, unsigned char );
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, signed char );
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, unsigned short );
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, signed short );
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, unsigned long );
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, signed long );
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, float );
> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, double );
>
> } // end namespace itk
>
> #endif
>
>
> On 28 December 2010 09:52, Ali Habib <ali.mahmoud.habib at gmail.com> wrote:
> > Dear All,
> > I need the pixel data as unsigned char* , I created my pipeline but I
> stuck
> > on how to get the buffer data , also I need to know does the pixel_value
> > will show me if the input is scaler or not
> > the code I use is :
> > typedef signed short InputPixelType;
> > const unsigned int InputDimension = 2;
> > typedef itk::Image< InputPixelType, InputDimension > InputImageType;
> > typedef itk::ImageFileReader< InputImageType > ReaderType;
> > typedef InputImageType::SizeType SizeType;
> > ReaderType::Pointer reader = ReaderType::New();
> > reader->SetFileName( "4.dcm" );
> > typedef itk::GDCMImageIO ImageIOType;
> > ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
> > reader->SetImageIO( gdcmImageIO );
> > try
> > {
> > reader->Update();
> > }
> > catch (itk::ExceptionObject & e)
> > {
> > std::cerr << "exception in file reader " << std::endl;
> > std::cerr << e << std::endl;
> > // return EXIT_FAILURE;
> > }
> > InputImageType::Pointer image_1 = reader->GetOutput() ;
> > // the image parameters
> > unsigned long lwidth = image_1->GetLargestPossibleRegion().GetSize()[0] ;
> > unsigned long lheight = image_1->GetLargestPossibleRegion().GetSize()[1]
> ;
> > InputImageType::IndexType index;
> > index[0]=1;
> > index[1]=1;
> > signed short pixel_value;
> > pixel_value= image_1->GetPixel( index );
>
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